Unusual biology across a group comprising more than 15% of domain Bacteria
Abstract
All rights reserved. A prominent feature of the bacterial domain is a radiation of major lineages that are defined as candidate phyla because they lack isolated representatives. Bacteria from these phyla occur in diverse environments and are thought to mediate carbon and hydrogen cycles. Genomic analyses of a few representatives suggested that metabolic limitations have prevented their cultivation. Here we reconstructed 8 complete and 789 draft genomes from bacteria representing >35 phyla and documented features that consistently distinguish these organisms from other bacteria. We infer that this group, which may comprise >15% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR). All CPR genomes are small and most lack numerous biosynthetic pathways. Owing to divergent 16S ribosomal RNA (rRNA) gene sequences, 50-100% of organisms sampled from specific phyla would evade detection in typical cultivation-independent surveys. CPR organisms often have self-splicing introns and proteins encoded within their rRNA genes, a feature rarely reported in bacteria. Furthermore, they have unusual ribosome compositions. All are missing a ribosomal protein often absent in symbionts, and specific lineages are missing ribosomal proteins and biogenesis factors considered universal in bacteria. This implies different ribosome structures and biogenesis mechanisms,more »
- Authors:
-
- Univ. of California, Berkeley, CA (United States)
- The Ohio State Univ., Columbus, OH (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1512215
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature (London)
- Additional Journal Information:
- Journal Name: Nature (London); Journal Volume: 523; Journal Issue: 7559; Journal ID: ISSN 0028-0836
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Brown, Christopher T., Hug, Laura A., Thomas, Brian C., Sharon, Itai, Castelle, Cindy J., Singh, Andrea, Wilkins, Michael J., Wrighton, Kelly C., Williams, Kenneth H., and Banfield, Jillian F. Unusual biology across a group comprising more than 15% of domain Bacteria. United States: N. p., 2015.
Web. doi:10.1038/nature14486.
Brown, Christopher T., Hug, Laura A., Thomas, Brian C., Sharon, Itai, Castelle, Cindy J., Singh, Andrea, Wilkins, Michael J., Wrighton, Kelly C., Williams, Kenneth H., & Banfield, Jillian F. Unusual biology across a group comprising more than 15% of domain Bacteria. United States. https://doi.org/10.1038/nature14486
Brown, Christopher T., Hug, Laura A., Thomas, Brian C., Sharon, Itai, Castelle, Cindy J., Singh, Andrea, Wilkins, Michael J., Wrighton, Kelly C., Williams, Kenneth H., and Banfield, Jillian F. Mon .
"Unusual biology across a group comprising more than 15% of domain Bacteria". United States. https://doi.org/10.1038/nature14486. https://www.osti.gov/servlets/purl/1512215.
@article{osti_1512215,
title = {Unusual biology across a group comprising more than 15% of domain Bacteria},
author = {Brown, Christopher T. and Hug, Laura A. and Thomas, Brian C. and Sharon, Itai and Castelle, Cindy J. and Singh, Andrea and Wilkins, Michael J. and Wrighton, Kelly C. and Williams, Kenneth H. and Banfield, Jillian F.},
abstractNote = {All rights reserved. A prominent feature of the bacterial domain is a radiation of major lineages that are defined as candidate phyla because they lack isolated representatives. Bacteria from these phyla occur in diverse environments and are thought to mediate carbon and hydrogen cycles. Genomic analyses of a few representatives suggested that metabolic limitations have prevented their cultivation. Here we reconstructed 8 complete and 789 draft genomes from bacteria representing >35 phyla and documented features that consistently distinguish these organisms from other bacteria. We infer that this group, which may comprise >15% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR). All CPR genomes are small and most lack numerous biosynthetic pathways. Owing to divergent 16S ribosomal RNA (rRNA) gene sequences, 50-100% of organisms sampled from specific phyla would evade detection in typical cultivation-independent surveys. CPR organisms often have self-splicing introns and proteins encoded within their rRNA genes, a feature rarely reported in bacteria. Furthermore, they have unusual ribosome compositions. All are missing a ribosomal protein often absent in symbionts, and specific lineages are missing ribosomal proteins and biogenesis factors considered universal in bacteria. This implies different ribosome structures and biogenesis mechanisms, and underlines unusual biology across a large part of the bacterial domain.},
doi = {10.1038/nature14486},
journal = {Nature (London)},
number = 7559,
volume = 523,
place = {United States},
year = {Mon Jun 15 00:00:00 EDT 2015},
month = {Mon Jun 15 00:00:00 EDT 2015}
}
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Figures / Tables:
Figure 1: Phylogeny and genomic sampling of the CPR. a, b, Subsets of a maximum-likelihood 16S rRNA gene phylogeny (Supplementary Fig. 1 ) showing the CPR, a monophyletic radiation of candidate phyla (a), and genomic sampling of candidate phyla (b). Proposed names for phyla within the superphyla Parcubacteria and Microgenomatesmore »
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